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Crystal structure of the ZO-1 PDZ1 domain in complex with the 7-mer Claudin2 C-terminal tail
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 2.0 M NAF, 0.1 M NAAC PH 4.6
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.351 α = 90 b = 72.17 β = 90 c = 76.958 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2013-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.79 30 99.2 0.07 16.78 7.4 22067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.9 95.1 0.42 2.34 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2H3M 1.79 26.322 20866 1125 98.79 0.20086 0.19817 0.2071 0.25356 0.2604 RANDOM 23.881
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.45 0.41 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.187 r_dihedral_angle_4_deg 23.653 r_dihedral_angle_3_deg 14.526 r_dihedral_angle_1_deg 6.528 r_long_range_B_refined 5.882 r_long_range_B_other 5.65 r_scangle_other 2.48 r_scbond_it 1.562 r_scbond_other 1.562 r_angle_refined_deg 1.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.187 r_dihedral_angle_4_deg 23.653 r_dihedral_angle_3_deg 14.526 r_dihedral_angle_1_deg 6.528 r_long_range_B_refined 5.882 r_long_range_B_other 5.65 r_scangle_other 2.48 r_scbond_it 1.562 r_scbond_other 1.562 r_angle_refined_deg 1.561 r_mcangle_it 1.397 r_mcangle_other 1.396 r_mcbond_it 0.864 r_mcbond_other 0.864 r_angle_other_deg 0.821 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1577 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data scaling XDS data reduction MOLREP phasing